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Inbreeding reduces long-term growth of Alpine ibex populations

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Abstract and Figures

Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species routinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial. Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly 100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in harsher environments. Populations with high average inbreeding (F ≈ 0.2) had population growth rates reduced by 71% compared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to guard against inbreeding effects in populations of endangered species have not been misplaced.
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1Department of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland. 2Department of Mathematical Sciences,
Norwegian University of Science and Technology, Trondheim, Norway. 3Department of Integrative Biology, University of Wisconsin-Madison, Madison,
WI, USA. 4Zoological Museum, University of Zurich, Zurich, Switzerland. 5Present address: Wildlife Analysis GmbH, Zurich, Switzerland. 6These authors
contributed equally: Claudio Bozzuto, Iris Biebach. *e-mail:;
Inbreeding depression, the harmful effects of inbreeding on the
fitness of individuals, is widespread among plants and animals,
with recent genomic studies revealing an even greater impact
on individual fitness than previously thought1. However, reduced
fitness of individuals due to inbreeding does not necessarily lead
to reduced population growth rates24, in the same way that natu-
ral selection need not impact population growth5. Instead, theory
predicts that the degree to which inbreeding depression affects
population growth will depend on the ecology and life history of a
species3,6. For example, in species experiencing density-dependent
population growth, even substantial inbreeding depression at the
individual level need not translate into reduced population growth,
because fitness reductions caused by inbreeding may be compen-
sated by fitness gains caused by relaxed competition. Under such
circumstances, inbred individuals may produce enough offspring to
maintain population growth (soft selection2).
Collecting unequivocal evidence for population-level effects of
inbreeding is difficult, because it requires many replicated popu-
lations that differ in levels of inbreeding to be monitored over
many generations. Hence, the extent of population-level effects of
inbreeding in the wild remains controversial79, and we currently
lack an understanding of the magnitude of the consequences of
inbreeding depression for long-term population growth in natural
populations10. Here, we take advantage of a long-term dataset of 26
reintroduced Alpine ibex populations (Supplementary Figs. 1 and
2) spanning 23–96 years to show that inbreeding can reduce long-
term population growth rates in the wild.
Alpine ibex were extirpated from the Alps by the end of the
nineteenth century, with only a single population surviving in the
Gran Paradiso region in northern Italy11. Starting in 1906, Alpine
ibex were taken from Gran Paradiso, bred in Swiss zoos and then
released back into their former habitat. These reintroductions are
well documented12, with counts of the released individuals, sub-
sequent time series of annual abundance counts and counts of the
numbers of harvested animals (Supplementary Table 1). Genetic
data suggest little natural migration between populations after rein-
troductions ceased13, making the populations distinct replicates for
the purpose of this study.
The ibex populations in our study experienced up to four rein-
troduction-associated bottlenecks13. The first bottleneck occurred
when the Swiss breeding programme was initiated with ~88 indi-
viduals from Gran Paradiso11. First reintroductions into the wild
with ibex from the Swiss breeding programme caused a second set
of bottlenecks (founder population sizes: 18–78). The third set of
bottlenecks took place when individuals from the first founder pop-
ulations were used to found additional wild populations (founder
population sizes: 9–137). Subsequent reintroductions sourced some
founder individuals from populations that had already experienced
three bottlenecks, thus causing a fourth bottleneck13. Genetically,
the bottlenecks were twice as pronounced as expected from the
number of released founders because, on average, only about half of
the founders contributed genes to the following generations14.
These serial bottlenecks resulted in considerable genetic drift
and inbreeding15. In this study, we use the term inbreeding to refer
to the average identity by descent across individuals that accumu-
lates under random mating in a population of finite size in con-
cert with genetic drift16,17. We quantified this inbreeding using 37
microsatellite loci and population-specific FST estimates that mea-
sure the probability of identity by descent of pairs of alleles at a
locus within populations relative to pairs of alleles from different
populations18,19. Population-specific FST estimates were calculated
for each population individually. Averaged across all populations,
they yield the familiar global FST estimate19. There is no evidence for
inbreeding due to non-random mating within Alpine ibex popula-
tions (FIS 0); therefore, population-specific FST estimates quantify
total inbreeding since the last common ancestral population18,20 at
the beginning of the reintroduction programme about 12.5 genera-
tions ago13. Population-specific FST does not suffer from the same
lack of power as individual inbreeding coefficients estimated from
limited molecular data10,15, because limited dispersal and population
Inbreeding reduces long-term growth of Alpine
ibex populations
Claudio Bozzuto 1,5,6, Iris Biebach 1,6, Stefanie Muff 1,2, Anthony R. Ives 3* and Lukas F. Keller 1,4*
Many studies document negative inbreeding effects on individuals, and conservation efforts to preserve rare species rou-
tinely employ strategies to reduce inbreeding. Despite this, there are few clear examples in nature of inbreeding decreasing
the growth rates of populations, and the extent of population-level effects of inbreeding in the wild remains controversial.
Here, we take advantage of a long-term dataset of 26 reintroduced Alpine ibex (Capra ibex ibex) populations spanning nearly
100 years to show that inbreeding substantially reduced per capita population growth rates, particularly for populations in
harsher environments. Populations with high average inbreeding (F 0.2) had population growth rates reduced by 71% com-
pared with populations with no inbreeding. Our results show that inbreeding can have long-term demographic consequences
even when environmental variation is large and deleterious alleles may have been purged during bottlenecks. Thus, efforts to
guard against inbreeding effects in populations of endangered species have not been misplaced.
NATURE ECOLOGY & EVOLUTION | VOL 3 | SEPTEMBER 2019 | 1359–1364 | 1359
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Supplementary resource (1)

... Genetic diversity will decline in populations subject to reductions in size and increased isolation through genetic drift, increased inbreeding, and reduced gene flow (Schlaepfer et al., 2018;Wright, 1931). These genetic changes can occur rapidly in low vagility species with small populations and can contribute to extinction risks (Bozzuto et al., 2019;Gilpin & Soulé, 1986;Saccheri et al., 1998;Spielman et al., 2004). Genetic sampling can help identify populations with low or declining genetic diversity for management and enhancement. ...
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Abstract Habitat loss and fragmentation can lead to smaller and more isolated populations and reduce genetic diversity and evolutionary potential. Conservation programs can benefit from including monitoring of genetic factors in fragmented populations to help inform restoration and management. We assessed genetic diversity and structure among four major populations of the Cactus Wren (Campylorhynchus brunneicapillus) in San Diego County in 2011–2012 and again in 2017–2019, using 22 microsatellite loci. We found a significant decline in heterozygosity in one population (San Pasqual) and a decline in allelic richness and effective population size in another (Sweetwater). Genetic diversity in the remaining two populations was not significantly different over time. Local diversity declined despite evidence of dispersal among some populations. Approximately 12% of genetically determined family groups (parents, offspring, siblings) included one or more members sampled in different territories with distances ranging from 0.2 to 10 km. All but one inferred dispersal events occurred within the same genetic population. Population structure remained relatively stable, although genetic differentiation tended to increase in the later sampling period. Simulations suggest that at currently estimated effective sizes, populations of Cactus Wrens will continue to lose genetic diversity for many generations, even if gene flow among them is enhanced. However, the rate of loss of heterozygosity could be reduced with increased gene flow. Habitat restoration may help bolster local population sizes and allelic richness over the long term, whereas translocation efforts from source populations outside of San Diego may be needed to restore genetic diversity in the short term.
... An alpine species with currently low genetic diversity, high mutation load, high levels of inbreeding and signs of inbreeding depression, is the Alpine ibex (Capra ibex) (Biebach & Keller, 2009;Bozzuto et al., 2019;Brambilla et al., 2018;Grossen et al., 2018;Grossen et al., 2020). Historic records suggest that Alpine ibex were intensely hunted, presumably since the 15th century and encountered their most severe bottleneck in the 19th century. ...
Full-text available
Population bottlenecks can have dramatic consequences for the health and long‐term survival of a species. Understanding of historic population size and standing genetic variation prior to a contraction allows estimating the impact of a bottleneck on the species genetic diversity. Although historic population sizes can be modelled based on extant genomics, uncertainty is high for the last 10‐20 millenia. Hence, integrating ancient genomes provides a powerful complement to retrace the evolution of genetic diversity through population fluctuations. Here, we recover 15 high‐quality mitogenomes of the once nearly extinct Alpine ibex spanning 8601 BP to 1919 CE and combine these with 60 published modern whole genomes. Coalescent demography simulations based on modern whole genomes indicate population fluctuations coinciding with the last major glaciation period. Using our ancient and historic mitogenomes, we investigate the more recent demographic history of the species and show that mitochondrial haplotype diversity was reduced to a fifth of the pre‐bottleneck diversity with several highly differentiated mitochondrial lineages having co‐existed historically. The main collapse of mitochondrial diversity coincides with elevated human population growth during the last 1‐2 kya. After recovery, one lineage was spread and nearly fixed across the Alps due to recolonization efforts. Our study highlights that a combined approach integrating genomic data of ancient, historic and extant populations unravels major long‐term population fluctuations from the emergence of a species through its near extinction up to the recent past.
... kakapo [85]; rattle snakes [86]; wolves [83]; killer whales [87]), while some studies show that decreased survival and population growth rate are correlated with higher inbreeding and mutation load (e.g. see arctic foxes [88] and alpine ibex [89]). Unfortunately, our understanding of the functional effects of specific mutations and their impacts on fitness in endangered species remains poor. ...
Full-text available
Unprecedented advances in sequencing technology in the past decade allow a better understanding of genetic variation and its partitioning in natural populations. Such inference is critical to conservation: to understand species biology and identify isolated populations. We review empirical population genetics studies of Endangered Bengal tigers within India, where 60–70% of wild tigers live. We assess how changes in marker type and sampling strategy have impacted inferences by reviewing past studies, and presenting three novel analyses including a single-nucleotide polymorphism (SNP) panel, genome-wide SNP markers, and a whole-mitochondrial genome network. At a broad spatial scale, less than 100 SNPs revealed the same patterns of population clustering as whole genomes (with the exception of one additional population sampled only in the SNP panel). Mitochondrial DNA indicates a strong structure between the northeast and other regions. Two studies with more populations sampled revealed further substructure within Central India. Overall, the comparison of studies with varied marker types and sample sets allows more rigorous inference of population structure. Yet sampling of some populations is limited across all studies, and these should be the focus of future sampling efforts. We discuss challenges in our understanding of population structure, and how to further address relevant questions in conservation genetics. This article is part of the theme issue ‘Celebrating 50 years since Lewontin's apportionment of human diversity’.
... Increased inbreeding may be accompanied by population decline in small populations (Bozzuto et al. 2019;Chen et al. 2016;Feng et al. 2019), which can drive populations to extinction (O'Grady et al. 2006;Saccheri et al. 1998;Wright et al. 2007;Niskanen et al. 2020) showed that inbreeding depression in adult sparrows in our study system varied little across years or across the different island environments inhabited by these house sparrows. Hence, the strength of inbreeding depression is similar between populations, but due to harboring more inbred individuals, the relative effect is stronger in smaller populations . ...
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Inbreeding can have negative effects on survival and reproduction, which may be of conservation concern in small and isolated populations. However, the physiological mechanisms underlying inbreeding depression are not well-known. The length of telomeres, the DNA sequences protecting chromosome ends, has been associated with health or fitness in several species. We investigated effects of inbreeding on early-life telomere length in two small island populations of wild house sparrows ( Passer domesticus ) known to be affected by inbreeding depression. Using genomic measures of inbreeding we found that inbred nestling house sparrows ( n = 371) have significantly shorter telomeres. Using pedigree-based estimates of inbreeding we found a tendency for inbred nestling house sparrows to have shorter telomeres ( n = 1195). This negative effect of inbreeding on telomere length may have been complemented by a heterosis effect resulting in longer telomeres in individuals that were less inbred than the population average. Furthermore, we found some evidence of stronger effects of inbreeding on telomere length in males than females. Thus, telomere length may reveal subtle costs of inbreeding in the wild and demonstrate a route by which inbreeding negatively impacts the physiological state of an organism already at early life-history stages.
... However, once reduced and fragmented, populations are likely to be recovering with diminished genetic diversity and often face poor genetic connectivity (Frankham, 1996). This was the case for the Alpine ibex (Capra ibex ibex) that underwent stepwise re-introductions from very small founder populations that had been subjected to serial bottleneck events (Biebach & Keller, 2010) and where high levels of inbreeding are reducing long-term population growth (Bozzuto et al., 2019). Aside from human interventions, species often naturally restore their population sizes as they disperse and recolonize previously inhabited territories (Sommer & Nadachowski, 2006). ...
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In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad‐scale geographic origin assignment using nuclear markers to support law enforcement. After 19th century extirpation, the European roe deer naturally recolonized Switzerland. Using mitochondrial and nuclear DNA markers, we demonstrate that Swiss roe deer had natural, multidirectional immigration from neighboring countries and that there is evidence of weak genetic differentiation within Switzerland among topographic regions.
This comprehensive species‑specific chapter covers all aspects of the biology of Alpine ibex Capra ibex, including paleontology, physiology, genetics, life history, ecology, habitat, diet, and behavior. The economic significance and management of Alpine ibex and future challenges for research and conservation are addressed as well. The chapter includes a distribution map, a photograph of the animal, and a list of key literature.
Climate change is expected to have a major hydrological impact on the core breeding habitat and migration corridors of many amphibians in the twenty-first century. The Yosemite toad (Anaxyrus canorus) is a species of meadow-specializing amphibian endemic to the high-elevation Sierra Nevada Mountains of California. Despite living entirely on federal lands, it has recently faced severe extirpations, yet our understanding of climatic influences on population connectivity is limited. In this study, we used a previously published double-digest RADseq dataset along with numerous remotely sensed habitat features in a landscape genetics framework to answer two primary questions in Yosemite National Park: (1) Which fine-scale climate, topographic, soil, and vegetation features most facilitate meadow connectivity? (2) How is climate change predicted to influence both the magnitude and net asymmetry of genetic migration? We developed an approach for simultaneously modeling multiple toad migration paths, akin to circuit theory, except raw environmental features can be separately considered. Our workflow identified the most likely migration corridors between meadows and used the unique cubist machine learning approach to fit and forecast environmental models of connectivity. We identified the permuted modeling importance of numerous snowpack-related features, such as runoff and groundwater recharge. Our results highlight the importance of considering phylogeographic structure, and asymmetrical migration in landscape genetics. We predict an upward elevational shift for this already high-elevation species, as measured by the net vector of anticipated genetic movement, and a north-eastward shift in species distribution via the network of genetic migration corridors across the park.
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The Alpine ibex (Capra ibex) is a mountain ungulate living in the European Alps. Although being currently classified as a species of Least Concern (LC) by the IUCN, a potential threat for its long-term conservation is introgression following hybridization with domestic goats (Capra hircus). Hybridization has been documented in Switzerland in captive and free ranging animals, although accurate data to assess the extent of this phenomenon in natural conditions in the Alps are lacking. Using an online survey and a network of experts, we collected and mapped unpublished evidence of hybridization events that occurred between Alpine ibex and feral domestic goats from 2000 to 2021. The results of this study showed that hybrids are distributed in most of the Alpine countries, and their presence is not a sporadic event, with some clusters including 4–20 probable hybrids. Our results illustrated the need for establishing a standardized and effective protocol to identify hybrids in the field (such as a formal description of the morphological traits characterizing hybrids), as well as clear guidelines for hybrid management. Even more importantly, this study also highlighted the need for actions aimed at avoiding hybridization, such as the effective management of domestic herds grazing in Alpine ibex core areas.
Thirty-nine endangered brush-tailed rock-wallabies (Petrogale penicillata) were reintroduced to Grampians National Park, western Victoria, between 2008 and 2012. Subsequent high mortality, low breeding, and no recruitment were linked to fox predation and physical disturbance during monitoring. From 2014 to 2017, the colony was left undisturbed and monitored only by remote camera. Five adult animals were identified across this period (1 ♂ and 3 ♀s – all tagged; and one untagged female), and an average of 0.7 pouch young were birthed per tagged female per year. In 2019, camera-monitoring and non-invasive genetic monitoring (faecal) were used to identify colony members, genetic diversity, and breeding. Camera monitoring in 2019 identified the same five individuals, whereas genetic monitoring using 12 microsatellites identified eight individuals (two male and six female genotypes). Genetic diversity within the colony was moderate (expected heterozygosity (He) = 0.655, observed heterozygosity (Ho) = 0.854). Leaving the colony undisturbed after 2013 correlated with improved adult survival, increased breeding, and successful recruitment of young to the population. Recommendations for the Grampians colony include continuation of regular camera- and scat monitoring to improve our understanding of the reintroduction biology of P. penicillata and other marsupials in open, unfenced landscapes.
Although human fragmentation of freshwater habitats is ubiquitous, the genetic consequences of isolation and a roadmap to address them are poorly documented for most fishes. This is unfortunate, because translocation for genetic rescue could help mitigate problems. We used genetic data (32 SNPs) from 203 populations of westslope cutthroat trout to (1) document the effect of fragmentation on genetic variation and population structure, (2) identify candidate populations for genetic rescue, and (3) quantify the potential benefits of strategic translocation efforts. Human-isolated populations had substantially lower genetic variation and elevated genetic differentiation, indicating that many populations are strongly influenced by random genetic drift. Based on simple criteria, 23 populations were candidates for genetic rescue, which represented a majority (51%) of suitable populations in one major region (Missouri drainage). Population genetic theory suggests that translocation of a small number of individuals (~5 adults) from nearby populations could dramatically increase heterozygosity by up to 58% (average across populations). This effort provides a clear template for future conservation of westslope cutthroat trout, while simultaneously highlighting the potential need for similar efforts in many freshwater species.
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Many population genetic activities, ranging from evolutionary studies to association mapping to forensic identification, rely on appropriate estimates of population structure or relatedness. All applications require recognition that quantities with an underlying meaning of allelic dependence are not defined in an absolute sense, but instead are made "relative to" some set of alleles other than the target set. The 1984 Weir and Cockerham FST estimate made explicit that the reference set of alleles was across populations, whereas standard kinship estimates do not make the reference explicit. Weir and Cockerham stated that their FST estimates were for independent populations, and standard kinship estimates have an implicit assumption that pairs of individuals in a study sample, other than the target pair, are unrelated or are not inbred. However, populations lose independence when there is migration between them, and dependencies between pairs of individuals in a population exist for more than one target pair. We have therefore re-cast our treatments of population structure, relatedness and inbreeding to make explicit that the parameters of interest involve the differences in degrees of allelic dependence between the target and the reference sets of alleles and so can be negative. We take the reference set to be the population from which study individuals have been sampled. We provide simple moment estimates of these parameters, phrased in terms of allelic matching within and between individuals for relatedness and inbreeding, or within and between populations for population structure. A multi-level hierarchy of alleles within individuals, alleles between individuals within populations, and alleles between populations allows a unified treatment of relatedness and population structure. We expect our new measures to have a wide range of applications, but we note that their estimates are sensitive to rare or private variants: some population-characterization applications suggest exploiting those sensitivities whereas estimation of relatedness may best use all genetic markers without filtering on minor allele frequency.
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Restoration of lost species ranges to their native distribution is key for the survival of endangered species. However, reintroductions often fail and long-term genetic consequences are poorly understood. Alpine ibex (Capra ibex) are wild goats that recovered from <100 individuals to ~50,000 within a century by population reintroductions. We analyzed the population genomic consequences of the Alpine ibex reintroduction strategy. We genotyped 101'822 genome-wide single nucleotide polymorphism loci in 173 Alpine ibex, the closely related Iberian ibex (Capra pyrenaica) and domestic goat (Capra hircus). The source population of all Alpine ibex maintained genetic diversity comparable to Iberian ibex, which experienced less severe bottlenecks. All reintroduced Alpine ibex populations had individually and combined lower levels of genetic diversity than the source population. The reintroduction strategy consisted of primary reintroductions from captive-breeding and secondary reintroductions from established populations. This step-wise reintroduction strategy left a strong genomic footprint of population differentiation, which increased with subsequent rounds of reintroductions. Furthermore, analyses of genome-wide runs of homozygosity showed recent inbreeding primarily in individuals of reintroduced populations. We showed that despite the rapid census recovery, Alpine ibex carry a persistent genomic signature of their reintroduction history. We discuss how genomic monitoring can serve as an early indicator of inbreeding. This article is protected by copyright. All rights reserved.
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A fascinating laboratory experiment by Hufbauer et al. (1) manipulates genetic diversity and population size of flour beetles (Tribolium castaneum) in the face of a change in the resource base offered in experimental microcosms. The experiment finds that extinction risk is offset to a comparable degree by adding a few genetically diverse individuals or by more substantially elevating population size with individuals drawn from the same source pool as the experimental population, leading the authors to argue that conservation of at-risk populations is most efficiently achieved by enhancing genetic diversity. This conclusion is in stark contrast, however, to that of a previously published 12-generation field experiment with an intertidal kelp (Postelsia palmeaformis; the sea palm), which followed extinction risk in free-living populations after independently manipulating population size and genetic diversity, and found overwhelming effects of demographic processes relative to genetic diversity (2). In light of the divergent conclusions and the important implications of these experiments for biodiversity conservation, an essential question is why these differences may have arisen.
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Wootton and Pfister (1) note the striking contrast between the results of their elegant field study (2) and our laboratory study (3), both of which manipulated genetic diversity and population size independently. Wootton and Pfister (1) found that population size most strongly influences extinction risk, whereas we (3) found that genetic diversity matters as much as population size in reducing extinction, and that genetic diversity also increases long-term growth rates of extant populations. Given the implications for management of small populations, it is crucial to understand why our results differ.
Inbreeding depression, the reduction of fitness caused by inbreeding, is a nearly universal phenomenon that depends on past mutation, selection, and genetic drift. Recent estimates suggest that its impact on individual fitness is even greater than previously thought. Genomic information is contributing to its detection and can enlighten important aspects of its genetic architecture. In natural populations, purging and genetic rescue mitigate fitness decline during inbreeding periods, and might be critical to population survival, thus, both mechanisms should be considered when assessing extinction risks. However, deliberate purging and genetic rescue involve considerable risk in the short and medium term, so that neither appears to be a panacea against high inbreeding depression.
Inbreeding depression (reduced fitness of individuals with related parents) has long been a major focus of ecology, evolution, and conservation biology. Despite decades of research, we still have a limited understanding of the strength, underlying genetic mechanisms, and demographic consequences of inbreeding depression in the wild. Studying inbreeding depression in natural populations has been hampered by the inability to precisely measure individual inbreeding. Fortunately, the rapidly increasing availability of high throughput sequencing data means it is now feasible to measure the inbreeding of any individual with high precision. Here, we review how genomic data are advancing our understanding of inbreeding depression in the wild. Recent results show that individual inbreeding and inbreeding depression can be measured more precisely with genomic data than via traditional pedigree analysis. Additionally, the availability of genomic data has made it possible to pinpoint loci with large effects contributing to inbreeding depression in wild populations, although this will continue to be a challenging task in many study systems due to low statistical power. Now that reliably measuring individual inbreeding is no longer a limitation, a major focus of future studies should be to more accurately quantify effects of inbreeding depression on population growth and viability. This article is protected by copyright. All rights reserved.
In the arguments in Chapter 3 leading to the Hardy-Weinberg principle, we found that, in order to obtain the actual genic structure sg, or genotypic structure Sg, of the population in a future generation g, we had to assume that the population was “infinitely” large.